Personal summary
I am a computational biologist working on understanding the forces that govern the interactions between organisms in ecologically critical environments, such as coral reefs, and the forces that drive major evolutionary transitions, such as the one that gave rise to the first photosynthetic Eukaryotas. I am also CEO of OceanOmics, a company dedicated to developing salable tools for environmental health monitoring.
Contact information
| left | Left |
|---|---|
| Department of Biochemistry and Microbiology, Rutgers University, USA | |
| ts942@sebs.rutgers.edu | |
| timothystephens.github.io | |
| TimothyStephens | |
| @timstep1383 |
Education and Research Experience
| year | what |
|---|---|
| 2019 — present | Post Doctoral Associate, Department of Biochemistry and Microbiology, Rutgers University |
| 2016 — 2019 | PhD, Institute for Molecular Bioscience, The University of Queensland |
| 2015 — 2015 | Honours, Institute for Molecular Bioscience, The University of Queensland |
| 2012 — 2015 | Bachelor of Biotechnology, Institute for Molecular Bioscience, The University of Queensland |
Awards and honours
| year_begin | what |
|---|---|
| 2023 | Selected to attend and present at the New Phytologist Next Generation Scientists Conference 2023, National University of Singapore |
| 2021 | 2019 Dean’s Award for Outstanding Higher Degree by Research Theses, University of Queensland |
| 2016 | Research Training Program (RTP) scholarship, University of Queensland |
| 2012 | Dean’s Commendation for Academic Excellence (achieved a GPA over 6.6), University of Queensland |
| 2011 | Merit Scholarship for academic achievement, University of Queensland |
Select Publications
| year | ref2print |
|---|---|
| 2024 | Benites L. F., Stephens T. G., Etten J. V., James T., Christian W. C., Barry K., Grigoriev I. V., McDermott T. R. & Bhattacharya D. Viruses associated with extremophilic red algal mats reveal signatures of early thermal adaptation. Communications Biology, 2024. [URL] |
| 2023 | Bhattacharya D., Stephens T. G., Chille E. E., Benites L. F., Chan C. X. Facultative lifestyle drives diversity of coral algal symbionts. Trends in Ecology and Evolution, 39(3):239-247, 2023. [URL] |
| 2023 | *Williams A., *Stephens T. G., Shumaker A., and Bhattacharya D. Peeling back the layers of coral holobiont multi-omics data. iScience, 26(9):107623, 2023. *Co-first authorship [URL] |
| 2023 | Stephens T. G., Strand E. L., Putnam H. M., and Bhattacharya D. Ploidy variation and its implications for reproduction and population dynamics in two sympatric Hawaiian coral species. Genome Biology and Evolution, evad149, 2023. [Preprint] [URL] |
| 2023 | Etten J. V, Stephens T. G., and Bhattacharya D. A k-mer-based approach for inferring phylogenetic relatedness of environmental genomic data. Systems Biology, syad037, 2023. Won the Publisher’s Award for Excellence in Systematic Research [URL] |
| 2023 | Etten J. V., Benites F. L., Stephens T. G., Yoon H. S., and Bhattacharya D. Algae obscura: The potential of rare species as model systems. Journal of Phycology, 59(2):293-300, 2023. [URL] |
| 2022 | Stephens T. G., Lee J., Jeong Y., Yoon H. S., Putnam H. M., Majerova E., and Bhattacharya D. High-quality genome assemblies from key Hawaiian coral species. GigaScience, 11:giac098, 2022. [URL] |
| 2022 | Benites L. F., Stephens T. G., and Bhattacharya D. Multiple waves of viral invasions in Symbiodiniaceae algal genomes. Virus Evolution, 8:veac101, 2022. [Preprint] [URL] |
| 2022 | Bhattacharya D., Etten J. V., Benites L. F., and Stephens T. G. Endosymbiotic ratchet accelerates divergence after organelle origin. BioEssays, e2200165, 2022. [URL] |
| 2022 | *Gabr A., *Stephens T. G., and Bhattacharya D. Loss of key endosymbiont genes may facilitate early host control of the chromatophore in Paulinella. iScience, 25:104974, 2022. *Co-first authorship [URL] |
| 2022 | Meng Z., Williams A., Liau P., Stephens T. G., Drury C., Chiles E. N., Su X., Javanmard M., and Bhattacharya D. Development of a portable toolkit to diagnose coral thermal stress. Scientific Reports, 12:14398, 2022. [URL] |
| 2022 | Bhattacharya D., Stephens T. G., Tinoco A., Richmond R., and Cleves P. A. Life on the edge: Hawaiian model for coral evolution. Limnology and Oceanography, 67:1976-1985, 2022. [URL] |
| 2022 | *Calatreva V., *Stephens T. G., Gabr A., Grossman A. R., and Bhattacharya D. Retrotransposition facilitated the establishment of a primary plastid in the thecate amoeba Paulinella. PNAS, 119:e2121241119, 2022. *Co-first authorship [URL] |
| 2022 | Dougan K. E., Gonzalez-Pech R. A., Stephens T. G., Shah S., Chen Y., Ragan M. A., Bhattacharya D., and Chan C. X. Genome-powered classification of microbial eukaryotes: focus on coral algal symbionts. Trends in Microbiology, 30:831-840, 2022. [URL] |
| 2021 | Williams A., Pathmanathan J. S., Stephens T. G., Su X., Chiles E. N., Conetta D., Putnam H. M., and Bhattacharya D. Multi-omic characterization of the thermal stress phenome in the stony coral Montipora capitata. PeerJ, 9:e12335, 2021. [Preprint] Featured by PeerJ Expert Curations: Molecular Ecology: PeerJ Expert Curations, PeerJ Blog [URL] |
| 2021 | Stephens T. G., Gabr A., Calatreva V., Grossman A. R., and Bhattacharya D. Why is primary endosymbiosis so rare?. New Phytologist, 231:1693-1699, 2021. [URL] |
| 2021 | Gonzalez-Pech, R. A., Stephens T. G., Chen Y., Mohamed A. R., Cheng Y., Shah S., Dougan K. E., Fortuin M. D. A., Lagorce R., Burt D. W., Bhattacharya D., Ragan M. A., and Chan C. X. Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium. BMC Biology, 0.842361111, 2021. [Preprint] [URL] |
| 2020 | Stephens T. G., Gonzalez-Pech R. A., Cheng Y., Mohamed A. R., Burt D. W., Bhattacharya D., Ragan M. A., and Chan C. X. Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions. BMC Biology, 18:56, 2020. [Preprint] Featured by IMB News [URL] |
| 2019 | Chen Y., Gonzalez-Pech R. A., Stephens T. G., Bhattacharya D., and Chan C. X. Evidence that inconsistent gene prediction can mislead analysis of dinoflagellate genomes. Journal of Phycology, 56:6-10, 2019. [Preprint] [URL] |
| 2018 | Stephens T. G., Ragan M. A., Bhattacharya D., and Chan C. X. Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions. Scientific Reports, 8:17175, 2018. [URL] |
| 2018 | Liu H., Stephens T. G., Gonzalez-Pech R. A., Beltran V. H., Lapeyre B., Bongaerts P., Cooke I., Aranda M., Bourne D. G., Foret S., Miller D. J., van Oppen M. J. H., Voolstra C. R., Ragan M.A., and Chan C.X. Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis. Communications Biology, 0.107638889, 2018. [Preprint] Featured by multiple outlets: IMB News, GBRF, Video Feature, IMB 2018 year in review [URL] |
Grants
| year_begin | what |
|---|---|
| 2023 | Rutgers TechAdvance Fund, $74,842 USD Funds to continue development of our coral health monitoring toolkit. Principal Investigators: Debashish Bhattacharya (Rutgers University), Rutgers University |
| 2023 | Core Facility Utilization Application, $5,000 USD Funds for metabolomic profiling of the sex hormone cycle in spawning corals. Principal Investigators: Debashish Bhattacharya (Rutgers University), Rutgers University |
| 2022 | Core Facility Utilization Application, $5,000 USD Funds for sequencing of coral microbiome samples. Principal Investigators: Debashish Bhattacharya (Rutgers University), Rutgers University |
| 2022 | Center for Nutrition, Microbiome, and Health Small Grant FY-22, $2,000 USD Characterizing the coral microbiome biogeography across colonies and reefs. Principal Investigators: Debashish Bhattacharya (Rutgers University), Center for Nutrition, Rutgers University |
| 2018 | UQ-FAPESP Strategic Research Fund SPRINT (2018/15159-9), $20,000 (~USD $14,000) Integrated genomic approaches to understand stress tolerance in bioethanol-producing yeasts and coral reef symbionts Principal Investigators: Cheong Xin Chan (UQ) and Jeferson Gross (State University of Sao Paulo), Jointly funded by University of Queensland (UQ) and Sao Paulo State Foundation (FAPESP) |
Teaching experience
| year | what |
|---|---|
| 2020 — present | Co-lecturer Rutgers University Design and conducted lectures on de novo next-generation genome and transcriptome sequencing, metabolomics, proteomics, metagenomics, phylogenetics, and phylogenomics in a join undergraduate and postgraduate course titled “Fundamentals of Microbial Genomics”. Duties include designing and marking student’ exam questions and oral presentations. |
| 2018 | Head Practical Tutor University of Queensland Duties included designing and developing assessment material for the course and organising marking of assignments. |
Selected Talks
| year_begin | what |
|---|---|
| 2023 | Stephens T. G., Etten J. V., Benites L. F., Mcdermott T., and Bhattacharya D. Cyanidiophyceae: The extremophilic red algae that underpin hot spring microbial communities in Yellowstone National Park. UQ Marine Ecogenomics Symposium 2023. 13-14 December 2023, University of Queensland, Australia. |
| 2023 | Stephens T. G., Calatrava V., Gabr A., Grossman A., and Bhattacharya D. Exploring the origin and evolution of primary plastids using Paulinella as a model system. International Society of Endocytobiology conference 2023. 10-14th September 2023, Field Museum, Chicago. |
| 2023 | Stephens T. G., Chille E., Strand E. L., Putnam H. M., and Bhattacharya D. Multi-omics investigation of coral resilience. Invited talk at Carnegie Plant Biology Seminar, August 2023. 25th August 2023, Carnegie Department of Plant Biology, Stanford University, USA. |
| 2023 | Stephens T. G., Calatrava V., Gabr A., Grossman A., and Bhattacharya D. Exploring the origin and evolution of primary plastids using Paulinella as a model system. New Phytologist Next Generation Scientists Conference 2023. 3rd July 2023, National University of Singapore, Singapore. |
| 2023 | Stephens T. G., Calatrava V., Gabr A., Grossman A., and Bhattacharya D. Exploring endosymbiosis and biotic interactions using niche, non-model algae. Invited talk at SCMB GenGen/ACE Special Seminar. 10th January 2023, The University of Queensland, Brisbane, Australia. |
| 2022 | Stephens T. G., Strand E. L., Putnam H. M., and Bhattacharya D. Differences in ploidy and the prevalence of clonal propagation between Montipora capitata and Pocillopora acuta from Kane’ohe Bay, Hawai’i. 15th International Coral Reef Symposium. 3-8th July 2022, Bremen, Germany. |
| 2022 | Stephens T. G., Etten J. V., McDermott T., and Bhattacharya D. Analysis of environmental meta-omics data from the extremophilic red algae Cyanidiophyceae. Joint Aquatic Sciences Meeting. 14-20th May, 2022, Grand Rapids, USA. |
| 2021 | Stephens T. G., Calatrava V., Gabr A., Grossman A., and Bhattacharya D. Insights into the evolution of a primary endosymbiosis through analysis of the Paulinella genome. 75th Annual Meeting of the Phycological Society of America. 13-22nd July 2021, online. |
| 2021 | Stephens T. G., Calatrava V., Gabr A., Grossman A., and Bhattacharya D. Insights into the evolution of a primary endosymbiosis through analysis of the Paulinella genome. 12th International Phycological Congress. 22-26th March 2021, Chile. |
Media coverage
| year_begin | what |
|---|---|
| 2024 | Our paper Multi-omic characterization of the thermal stress phenome in the stony coral Montipora capitata was featured as part of PeerJ Expert Curations: Molecular Ecology: PeerJ Expert Curations, PeerJ Blog |
| 2023 | Our paper A k-mer-Based Approach for Phylogenetic Classification of Taxa in Environmental Genomic Data won the Publisher’s Award for Excellence in Systematic Research |
| 2022 | Our paper Retrotransposition facilitated the establishment of a primary plastid in the thecate amoeba Paulinella covered by Rutgers Research |
| 2022 | Article by Rutgers Research on our short film The Coral Holobiont Response to Climate Change which won Best Trailer in the Kiez Berlin Film Festival. |
| 2021 | Our paper Why is primary endosymbiosis so rare? was covered by Rutgers Newsroom. We also produced two animated videos: Video 1, Video 2 |
| 2020 | Our paper Amoeba Genome Reveals Dominant Host Contribution to Plastid Endosymbiosis covered by Rutgers Today |
Service
| year | what |
|---|---|
| 2023 — present | Associate Editor: Symbiotic and Parasitic Protists section, Frontiers in Protistology |
Patents
| year | what |
|---|---|
| 2023 | Provisional Patent “Protein Markers of Coral Stress” (5431.1025-000:2023-098) Non-provisional US Patent filed 2024/03/27 |
| 2023 | Provisional Patent “Coral Rapid Strip Test” (5431.1024-000:2023-097) |